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Dispersal is a behavioral process that shuffles genes across the physical and social landscapes. Analysis of how genetic variation is structured hierarchically and among males versus females can provide insights into underlying dispersal processes, even when direct observations of dispersal events are lacking, but application of these techniques in primate studies has been limited. We investigated dispersal patterns in two South American primates — woolly and spider monkeys — using a combination of multilocus genotype data from > 150 animals sampled at two sites in Amazonian Ecuador and opportunistic field observations that shed light on likely dispersal events. Molecular analyses revealed considerable gene flow by females, but substantial male-mediated gene flow was also detected, particularly for woolly monkeys. In both taxa, the extent of population differentiation between the two study sites was greater for males than for females, indicating that gene flow by males has been more restricted historically. Additionally, in one group of spider monkeys, the average relatedness among adult males was significantly greater than that among females, consistent with strong male philopatry, and assignment tests for that group likewise suggest female-biased dispersal. However, for another group of spider monkeys — and for all groups of woolly monkey surveyed — these patterns were not observed. Our molecular results are concordant with field observations of immigrations by female spider monkeys, disappearances (likely emigrations) involving females of both species, and multiple sightings of solitary males and small bachelor groups in woolly monkeys, as well as with the specific dispersal histories of a few woolly monkey individuals discernable through longitudinal molecular sampling. Overall, the results demonstrate the utility of molecular approaches to studying dispersal in primates as a complement to observational studies, but also suggest that further evaluation of dispersal patterns among these primates is needed.